The nuclear pore complex (NPC) is a large, modular protein assembly that principally regulates nucleocytoplasmic transport in all eukaryotes. The ~60-120MDa NPC is a modular assembly of multiple copies of ~30 distinct proteins that are arranged into sub-complexes. The entire NPC is not amenable to high- resolution structural studies, due to its large size and intrinsic flexibility. However, using a divide and conquer approach we tackle this problem by taking advantage of the modular nature of the NPC and obtaining high- resolution structures of individual sub-complexes. As a first step towards understanding the detailed organization of the NPC, we propose to solve high-resolution structures of the NPC structural scaffold Y and Nic96 complex and to characterize their inter-complex interactions. Our preliminary results present a high-resolution complete composite structure of the Y-complex. We compare our results to previous low-resolution studies and highlight the importance of high-resolution structures of the scaffold sub-complexes. Previous structural studies have shown a strong evolutionary relationship between a number of Y and Nic96 complex components. Thus, by leveraging our experience with the structurally well-characterized Y complex, this proposal will focus on investigating the biochemical characteristics of the evolutionarily similar but less investigated Nic96 complex and elucidate its high-resolution structure. Concurrently, the inter-complex interactions between the Y and Nic96 complex will be established as a first step towards understanding their function and organization into the NPC. A detailed structure of the Nic96 complex and its interplay with the Y-complex will uncover the structural basis for the function of the NPC and the various diseases associated with scaffold components.